This study examined the effects of long-term frozen storage (-20 °C for 5 months) of free amino acids (FAAs) and nucleotide-related compounds (NRCs) in muscle and hepatopancreas of the coconut crab Birgus latro. Although long-term frozen storage had little effect on FAA composition in muscle, the amounts of several FAAs increased in the hepatopancreas that may be the result of protein decomposition during the frozen storage. Long-term storage at -20°C significantly increased the amounts of disodium 5ʹ-inosine monophosphate (IMP) in muscle and hepatopancreas, resulting from the deaminase activity of 5ʹ-adenosine monophosphate (AMP) which deaminates AMP to IMP. Changes in FAAs and NRCs may result in changes in the flavor of muscle and hepatopancreas of frozen stored coconut crabs, both through altered amounts of each substance and synergistic interactions among substances.